Biology Commons^™

The Role Of Semaphorins In Response To Injury In C. Elegans Neurons, Maria Belen Harreguy Alfonso

Dissertations

When neural tissue is injured by trauma, delicate neuronal processes such as axons and dendrites are prone to lesion damage and often disconnect. The molecular, cellular, and circuit mechanisms that underlie the regrowth and reconnection of these processes and the recovery of behavior are major challenges in the fields of neuroscience, regeneration, and resilience. At the molecular and cellular levels, signaling pathways that mediate neuronal growth cone guidance during development can play a role in neuronal regeneration and recovery from injury. One family of signaling proteins involved in this process comprises the highly conserved semaphorins and their receptors, the plexins. …

Sustainable Food House Area (Sfha): Analysis Of Community Knowledge And Behavior, Delvi Adri, Mimien Henie Irawati, Sueb Sueb

Jurnal Pendidikan Sains

This research aimed to assess the knowledge and behavior of the community regarding the Sustainable Reserve Food Garden (SRFG) program. The study was conducted in July 2016 in Jorong Lubuk Agam, Kenagarian Ampang Kuranji Koto Baru, Dharmasraya, West Sumatra. Utilizing a descriptive quantitative approach, data were collected using Accidental Random Sampling, involving 33 heads of families as respondents. The findings revealed that community knowledge and behavior related to the SRFG program were generally insufficient, with 44.1% and 47.27% of respondents, respectively, demonstrating a lack of understanding and practice. The study concludes that approximately one-third of the population has limited knowledge …

The Investigation Of The Antimicrobial And Biofilm-Disrupting Properties Of Synthesized Hemibastadin Derivatives, Antonio Harvey, Andrew A. Yeagley

Longwood Senior Thesis Proposal

We want to investigate structural changes to the core hemibastadin structure while attempting to make these derivatives biologically safer. Since these modifications have never been done before, we will need to design a synthesis of these new molecules. Due to the nature of the molecules (dimers), a divergent synthesis that allows for the creation of both halves simultaneously seems most appropriate. A successful synthesis of these compounds will allow us to further investigate these derivatives for their antimicrobial and biofilm-disrupting properties.

Consequences Of Spatial Structure In Soil–Geomorphic Data On The Results Of Machine Learning Models, Daehyun Kim, Insang Song, Lorrayne Miralha, Daniel R. Hirmas, Ryan W. Mcewan, Tom G. Mueller, Pavel Samonil

Biology Faculty Publications

In this paper, we examined the degree to which inherent spatial structure in soil properties influences the outcomes of machine learning (ML) approaches to predicting soil spatial variability. We compared the performances of four ML algorithms (support vector machine, artificial neural network, random forest, and random forest for spatial data) against two non-ML algorithms (ordinary least squares regression and spatial filtering regression). None of the ML algorithms produced residuals that had lower mean values or were less autocorrelated over space compared with the non-ML approaches. We recommend the use of random forest when a soil variable of interest is weakly …

Identification Of Scientific Argumentation Ability Of High School Students On Optical Instrument Material, Rais Muktamar Amin, Parno Parno, Sentot Kusairi, Marlina Ali

Jurnal Pendidikan Sains

Optical instruments play a crucial role in physics education, providing essential material for students to understand complex concepts. This study aims to evaluate the scientific argumentation abilities of high school students regarding optical instruments. Conducted as a quantitative descriptive study, the research involved 60 eleventh-grade MIPA students from SMA Laboratorium UM. The research instrument was a scientific argumentation test comprising 12 essay questions, designed according to the Toulmin Argumentation Pattern (TAP) adaptation indicators, with a reliability coefficient of 0.332. Student responses were classified into five levels of scientific argumentation based on the TAP model, as developed by Sampson, Enderle, and …

Identifying Students’ Incorrect Common-Sense Knowledge In Forces And Motion: Recommendations For Developing Computer-Based Learning Media, Ahmad Ridlotul Adha, Sutopo Sutopo, Nasikhuddin Nasikhuddin

Jurnal Pendidikan Sains

Conceptual understanding is a crucial area in physics education research, focusing on students’ comprehension of fundamental principles. Force and motion, integral topics within this field, are inherently linked to students’ daily experiences. Numerous studies have identified the persistence of common sense knowledge among students. This research presents a literature review aimed at identifying such consistently held misconceptions. We analyzed 17 papers sourced from Publish or Perish 8, Google Scholar, and Scopus. Our analysis revealed that the concepts of impetus and active force are the most persistent forms of common sense knowledge, influenced by real-life experiences. Additionally, students’ difficulties with kinematics …

Analyzing Physics Students’ Misconceptions About Simple Electrical Circuits, Sapta Adiguna, Shinta Dewi Susanti, Sentot Kusairi, Iwan Setiawan

Jurnal Pendidikan Sains

This study investigates the prevalence and types of misconceptions among first-year Physics Education students regarding simple electrical circuits using the Simple Electric Circuits Diagnostic Test (SECDT). Employing a quantitative descriptive approach, the research analyzes responses from a sample of 42 students, selected through convenience sampling. The SECDT, a three-tier diagnostic instrument with a reliability of 0.69, identifies student misconceptions by categorizing responses into scientific knowledge, misconceptions, no understanding, and lack of knowledge. The results indicate significant gender differences in the types and prevalence of misconceptions. Male students exhibited a higher percentage of misconceptions (77.5%) compared to female students (62.8%). Notably, …

The Influence Of Predict, Observe, And Explain (Poe) Learning Accompanied By Formative Assessment On Misconceptions And Mastery Of Students’ Concepts Of Temperature And Heat Material, Ahmad Ilmar, Sentot Kusairi, Khusaini Khusaini

Jurnal Pendidikan Sains

High misconceptions and students’ mastery of concepts that are low enough are detected in temperature and heat material. To overcome this, teachers must apply learning strategies that are able to actively involve students in observation activities, namely the POE learning strategy. However, POE learning is not always easy to apply, students are still weak in communicating the results of their experiments. Therefore, a way is needed that helps students during the learning process to be more confident and not afraid when asked to argue, namely with formative assessment. POE learning accompanied by formative assessment aims to enable students to understand …

Konsep Diagnosis Dan Penatalaksanaan Fraktur Osteoporosis Terkini, I Gusti Ngurah Wien Aryana, Febyan Febyan

Jurnal Penyakit Dalam Indonesia

Osteoporosis is a metabolic bone disease that is caused by a decreased amount of bone mass, and microarchitectural damage to bone tissue that affects the bone to break easily. Osteoporosis can be divided into primary and secondary etiologies. Vertebral, hip, distal radius, and proximal humerus are the most common predilection of fracture complication due to osteoporosis. The diagnosis of osteoporotic fractures is established based on the identification of risk factors, general clinical manifestations, specific manifestation from each fracture predilection, and advanced examinations, including radiology imaging and dual-energy x-ray absorptiometry. The purpose of osteoporotic fractures management in elderly is a stable …

Optimization Of The Bio-Synthesis Of Magnesium Nanoparticles From Staphylococcus Haemolyticus: A Pilot Study, Mariam Bassam, Malak Mezher, Mahmoud Khalil

BAU Journal - Science and Technology

Nanotechnology is developing rapidly. This field has many influences in humans’ life. Nanoparticles (NPs) have many unique properties including the size, shape, morphology, and surface area. The synthesis of NPs could be achieved by three ways: physical, chemical, and biological. However, the biological synthesis of NPs has a priority on the other domains due to its safety and environmental friendship. In this regard, the main objective of this study was to synthesize magnesium (Mg) NPs from the bacterium S. haemolyticus which was isolated from the Lebanese wastewater. Different parameters were applied to detect the best conditions to produce the highest …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Genome-Wide Search Algorithms For Identifying Dynamic Gene Co-Expression Via Bayesian Variable Selection, Wenda Zhang, Zichen Ma, Lianming Wang, Daping Fan, Yen Yi Ho

Faculty Publications

A wealth of gene expression data generated by high-throughput techniques provides exciting opportunities for studying gene-gene interactions systematically. Gene-gene interactions in a biological system are tightly regulated and are often highly dynamic. The interactions can change flexibly under various internal cellular signals or external stimuli. Previous studies have developed statistical methods to examine these dynamic changes in gene-gene interactions. However, due to the massive number of possible gene combinations that need to be considered in a typical genomic dataset, intensive computation is a common challenge for exploring gene-gene interactions. On the other hand, oftentimes only a small proportion of gene …

Classification Of Colon Cancer Patients Into Consensus Molecular Subtypes Using Support Vector Machines, Necla Koçhan, Baris Emre Dayanc

Turkish Journal of Biology

Background/aim: The molecular heterogeneity of colon cancer has made classification of tumors a requirement for effective treatment. One of the approaches for molecular subtyping of colon cancer patients is the Consensus Molecular Subtypes (CMS) developed by the Colorectal Cancer Subtyping Consortium (CRCSC). CMS-specific RNA-Seq dependent classification approaches are recent with relatively low sensitivity and specificity. In this study, we aimed to classify patients into CMS groups using RNA-seq profiles. Materials and methods: We first identified subtype specific and survival associated genes using Fuzzy C-Means (FCM) algorithm and log-rank test. Then we classified patients using Support Vector Machines with Backward Elimination …

Svm-Do: Identification Of Tumor-Discriminating Mrna Signatures Via Support Vectormachines Supported By Disease Ontology, Mustafa Erhan Özer, Pemra Özbek Sarica, Kazim Yalçin Arğa

Turkish Journal of Biology

Background/aim: The complicated nature of tumor formation makes it difficult to identify discriminatory genes. Recently, transcriptome-based supervised classification methods using support vector machines (SVMs) have become popular in this field. However, the inclusion of less significant variables in the construction of classification models can lead to misclassification. To improve model performance, feature selection methods such as enrichment analysis can be used to extract useful variable sets. The detection of genes that can discriminate between normal and tumor samples in the association of cancer and disease remains an area of limited information. We therefore aimed to discover novel and practical sets …

Compcorona: A Web Application For Comparative Transcriptome Analyses Ofcoronaviruses Reveals Sars-Cov-2-Specific Host Response, Rana Sali̇hoğlu, Fati̇h Saraçoğlu, Mustafa Si̇bai̇, Tali̇p Zengi̇n, Başak Abak Masud, Onur Karasoy, Tuğba Önal Süzek

Turkish Journal of Biology

Background/aim: Understanding the mechanism of host transcriptomic response to infection by the SARS-CoV-2 virus is crucial, especially for patients suffering from long-term effects of COVID-19, such as long COVID or pericarditis inflammation, potentially linked to side effects of the SARS-CoV-2 spike proteins. We conducted comprehensive transcriptome and enrichment analyses on lung and peripheral blood mononuclear cells (PBMCs) infected with SARS-CoV-2, as well as on SARS-CoV and MERS-CoV, to uncover shared pathways and elucidate their common disease progression and viral replication mechanisms. Materials and methods: We developed CompCorona, the first interactive online tool for visualizing gene response variance among the family …

Stemnesscore: An R Package To Estimate The Stemness Of Glioma Cancer Cells At Single-Cell Resolution, Necla Koçhan, Yavuz Oktay, Gökhan Karakülah

Turkish Journal of Biology

Background/aim: Glioblastoma is the most heterogeneous and the most difficult-to-treat type of brain tumor and one of the deadliest among all cancers. The high plasticity of glioma cancer stem cells and the resistance they develop against multiple modalities of therapy, along with their high heterogeneity, are the main challenges faced during treatment of glioblastoma. Therefore, a better understanding of the stemness characteristics of glioblastoma cells is needed. With the development of various single-cell technologies and increasing applications of machine learning, indices based on transcriptomic and/or epigenomic data have been developed to quantitatively measure cellular states and stemness. In this study, …

Suma: A Lightweight Machine Learning Model Powered Shared Nearest Neighbour Based Clustering Application Interface Of Scrna-Seq, Hamza Umut Karakurt, Pınar Pir

Turkish Journal of Biology

Background/aim: Single-cell transcriptomics (scRNA-Seq) explores cellular diversity at the gene expression level. Due to the inherent sparsity and noise in scRNA-Seq data and the uncertainty on the types of sequenced cells, effective clustering and cell type annotation are essential. The graph-based clustering of scRNA-Seq data is a simple yet powerful approach which presents data as a “shared nearest neighbour” graph and clusters the cells using graph clustering algorithms. These algorithms are dependent on several user-defined parameters. Here we present SUMA, a lightweight tool that uses a random forest model to predict the optimum number of neighbours to have the optimum …

Physicochemical Differences Between Camelid Single-Domain Antibodies And Mammalian Antibodies, Nazli Eda Eski̇er, Doğa Eski̇er, Esi̇n Fi̇ruzan, Si̇bel Kalyoncu

Turkish Journal of Biology

Background/aim: In recent years, single-domain antibodies, also known as nanobodies, have emerged as an alternative to full immunoglobulin Gs (IgGs), due to their various advantages including increased solubility, faster clearance, and cheaper production. Nanobodies are generally derived from the variable domain of the camelid heavy-chain-only immunoglobulin Gs (hcIgGs). Due to the high sequence homology between variable heavy chains of camelids (VHHs) and humans (VHs), hcIgGs are ideal candidates for nanobody development. However, further examination is needed to understand the structural differences between VHs and VHHs. This analysis is essential for nanobody engineering to mitigate potential immunogenicity while preserving stability, functionality, …

Deep Learning In Bioinformatics, Malik Yousef, Jens Allmer

Turkish Journal of Biology

Deep learning is a powerful machine learning technique that can learn from large amounts of data using multiple layers of artificial neural networks. This paper reviews some applications of deep learning in bioinformatics, a field that deals with analyzing and interpreting biological data. We first introduce the basic concepts of deep learning and then survey the recent advances and challenges of applying deep learning to various bioinformatics problems, such as genome sequencing, gene expression analysis, protein structure prediction, drug discovery, and disease diagnosis. We also discuss future directions and opportunities for deep learning in bioinformatics. We aim to provide an …

Lead In Paint-Contaminated Residential Soils With Varying Physicochemical Properties From Three Large Us Cities: Assessment Of Geochemical Forms And Recommendations On Amendments For Immobilization, Hadeer Saleh, Dibyendu Sarkar, Washington Braida, Steve Larson, Rupali Datta

Michigan Tech Publications

Lead in yard soils has been recognized as the principal source of excess lead absorption among young children. The hazard imposed by soil lead is dependent on the geochemical forms of lead in soils. Soil properties such as pH, soil organic matter, clay, and carbonate content influence the geochemical forms of lead in soil. This study was conducted to investigate the correlation between soil properties and the geochemical speciation of lead in lead paint-contaminated residential soils from three major US cities. A comprehensive field survey was conducted, involving the collection of soils from ten houses in each of the cities: …

Draft Genomes Of Lactobacillus Jensenii Umb0908, Umb1545, And Umb5777 From The Urinary Tract, Maria Steiling, Briana Jackson, Natalie Stegman, Cerena Sedano, Catherine Putonti

Biology: Faculty Publications and Other Works

Lactobacillus jensenii is a member of the female urogenital microbiome. Previous research has identified strains of L. jensenii that are capable of inhibiting or killing uropathogens, including E. coli. Here, we present the draft genomes of three L. jensenii strains collected from urine samples.

Draft Genome Sequences Of Lactobacillus Paragasseri Strains Isolated From The Female Urinary Tract, Briana Jackson, Natalie Stegman, Cerena Sedano, Maria Steiling, Catherine Putonti

Biology: Faculty Publications and Other Works

Lactobacillus species are often associated with a healthy environment in the female urogenital tract. Here, we present the draft genome assemblies for three L. paragasseri strains isolated from voided urine samples from females with type II diabetes; two of the strains were collected from the same individual 3 months apart.

Investigation Of The Deubiquitinating Enzyme Usp7 In The Brain, Hao Chen

Arts & Sciences Graduate Student Theses and Dissertations

The development of the nervous system relies on precise control of protein ubiquitination and degradation. Consequently, imbalance in the ubiquitin signaling network is believed to have significant implications for neurological disorders. Recent research has not only detailed the various functions of different ubiquitin ligases in neural development, but has also disclosed the role of deubiquitinating enzyme as an additional regulatory dimension in the ubiquitin signaling network. Specifically, deletion or mutation of the deubiquitinating enzyme USP7 causes the Hao-Fountain syndrome, characterized by developmental delay, intellectual disability, autism, and aggressive behavior. Although USP7 has been studied in proliferating cells in the context …

Discerning The Roles Of Novel Glycosyltransferases In The Pathogenic Yeast Cryptococcus Neoformans, Liza Loza

Arts & Sciences Graduate Student Theses and Dissertations

Cryptococcus neoformans (Cn) is an opportunistic fungal pathogen responsible for over 112,000 deaths each year. This yeast is ubiquitous in the environment, where it is particularly associated with soil, trees, and bird excreta. When a susceptible host inhales infectious particles, Cn can proliferate in the lungs before disseminating to the brain to cause an often-fatal meningoencephalitis. Cryptococcosis primarily afflicts those living with uncontrolled HIV/AIDS, accounting for ~15% of AIDS-related mortality. The antifungals available to treat this devastating disease are few in number, toxic to patients, and largely inaccessible in resource-limited settings. The major virulence factor of Cn is its complex …

Tfeb Degradation Is Regulated By An Ikk/Β-Trcp2 Phosphorylation-Ubiquitination Cascade, Yan Xiong

Arts & Sciences Graduate Student Theses and Dissertations

Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and autophagy that plays a key role in the regulation of cellular clearance pathways. TFEB is regulated via a complex array of post-translational modifications (PTMs), but the exact molecular mechanism that regulates TFEB stability has remained elusive. Here, we show that TFEB levels are critically regulated by a defined phosphorylation-ubiquitination cascade. A human kinome screen identifies IKK (inhibitor of κB kinase) as a TFEB modifier, and a combination of phosphorylation assays, mass spectrometry analyses, and site-specific mutagenesis unveils a previously unrecognized TFEB phospho-degron (423SPFPSLS429) as the target of IKK. …

A Dynamic Duo: Investigating The Interactions Between Xanthomonas Citri Pv. Malvacearum And Pseudomonas Syringae, Taylor Harris

Arts & Sciences Graduate Student Theses and Dissertations

Bacterial pathogens threaten crop production worldwide, which highlights the need to understand plant and pathogen interactions. Studies on plant-pathogen interactions typically focus on a single host and pathogen. However, bacteria exist in complex microbial communities, not alone. There are few studies that examine the mechanisms behind multi-pathogen infections which renders a gap in our understanding of the subsequent implications on agriculture. In this dissertation, I use in vitro plate assays with RNA-sequencing and in planta assays to investigate the interactions between two cotton bacterial pathogens, Xanthomonas citri pv. malvaearum (Xcm) and Pseudomonas syringae (Ps). In vitro plate assays demonstrate that …

A Quantum Physics-Based Force Field For Biomolecular Simulation, Roseane Dos Reis Silva

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation explores the development of a physics-based force field meticulously tailored to guide molecular dynamics simulations of biomolecules. At its core, the Hydrogen-like Intermolecular Polarizable Potential (HIPPO) force field emerges as an apex of achievement, devised to refine the precision of short-range intermolecular interactions. HIPPO's inception marks a profound stride towards heightened realism in molecular simulations, anchored in Quantum Physics theory and fortified by state-of-the-art Quantum Chemistry calculations. This force field's efficacy is attested by its systematic application in constructing models featuring diverse organic molecules, from water to benzene, and those with motifs resembling proteins and nucleic acids. HIPPO …

Following The Paper Trail: An Ethnoecology Of Hand Papermaking Traditions, James Ojascastro

Arts & Sciences Graduate Student Theses and Dissertations

Plants and their fibers have served as simple yet incredibly versatile raw materials for innovation for as long as humans have been on the planet. As the principal structural building blocks of plant cell walls, these hollow, cellulosic fibers have been co-opted by cultures around the world to meet diverse structural, absorptive, motile, and thermoregulatory needs—especially as textiles and paper. Despite (or because of!) this versatility, fibers vary considerably in physiology, and ethnographic records show that very few plant species have been chosen by tradition for use in fiber products. Surprisingly, no fiber ethnobotany study to date has attempted to …

Investigating The Relationship Between Smoking, Genomics, And Brain Imaging, Yoonhoo Chang

Arts & Sciences Graduate Student Theses and Dissertations

Cigarette smoking has been linked to adverse health outcomes, including several forms of cancer, respiratory and cardiovascular disease, and dementia. Despite the public health campaigns aimed at reducing tobacco use, the behavior remains prevalent, and its association with various organs is an active area of research. Recent studies showed that smoking behaviors have strong genetic contributions. Through genome-wide association studies, the genetic risk score of individuals can be created and used as a basis for more effective and precise healthcare solutions. Chapter 2 explores the creation of a polygenic risk score (PRS) for smoking cessation and its utility in two …

Apolipoprotein E Adopts An Antiparallel Dimer In Discoidal Lipoproteins, Michael Ray Strickland

Arts & Sciences Graduate Student Theses and Dissertations

Apolipoprotein E (ApoE) is the major lipoprotein in the central nervous system and forms high density lipoprotein (HDL) like lipoprotein. ApoE is primarily secreted by astrocytes in the central nervous system and is thought to play an important role in cholesterol and lipid transport. The APOE gene has three major alleles, APOE2, APOE3, and APOE4. These alleles encode for 3 common APOE protein isoforms, ApoE2, ApoE3, and ApoE4. APOE3 is most common isoform of APOE with the other two isoforms differing by the loss (ApoE4, Cys112Arg) or gain (ApoE2, Arg158Cys) of a cysteine residue. APOE4 is the largest risk factor …